Research workbench
Crystal structure of a ZIF23-GCN4 chimera bound to DNA
Analyse Crystal structure of a ZIF23-GCN4 chimera bound to DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LLM
- Type
- protein + DNA
- Length
- 198 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*CP*CP*CP*AP*CP*GP*CP*GP*TP*GP*GP*G)-3'; Chimera of ZIF23-GCN4
- UniProt
- P08046, P03069
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 62% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5'-D(*TP*CP*CP*CP*AP*CP*GP*CP*GP*TP*GP*GP*G)-3' | dna | 13 | — | — |
| C | Chimera of ZIF23-GCN4 | protein | 87 | 61% helix, 9% strand | P08046, P03069 |
| D | Chimera of ZIF23-GCN4 | protein | 85 | 62% helix, 9% strand | P08046, P03069 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.47 | 0.84 | 15 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1076 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 753 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–C · 704 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–B · 602 Ų buried · 53 hydrogen bonds · nucleic-nucleic
- B–D · 487 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 1LLM · Crystal Structure of a Zif23-GCN4 Chimera Bound to DNA · the same entry in another collection · chain D against D, TM-score 1.00
- P08046 · AlphaFold monomer V2.0 prediction for early growth response protein 1 (P08046) · a predicted model of the same protein · chain C against A, TM-score 0.71
- P03069 · AlphaFold monomer V2.0 prediction for general control transcription factor GCN4 (P03069) · a predicted model of the same protein · chain C against A, TM-score 0.47
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P08046
- Every structure of UniProt P03069
- Elsewhere: RCSB PDB 1LLM · PDBe 1LLM · UniProt P08046 · UniProt P03069
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